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John P. Cunningham

Publications and source records attributed to John P. Cunningham.

At least 19 recordsLinked to original sources
arXiv2026

Computation-Aware Kalman Filtering with Model Selection for Neural Dynamics

Due to their explicit priors and ability to model uncertainty, Bayesian methods have played a major role in dynamical latent variable modeling of single-cell neural recordings. However, modern-sized datasets have made overparameterized deep networks the preferred methods of choice due to their predictive power and favorable computational scaling. While many posterior approximations exist, all incur approximation errors. Recent work accounts for this error in the form of computational uncertainty but comes at the cost of quadratic complexity and assumes fixed model hyperparameters. Here we extend this development to model selection, including a novel training loss and optimization scheme, which yields tractable inference in large state-spaces. We introduce a framework, the Computation-Aware State-Space Model (CASSM), specifically designed for the scale-imbalanced regime, where the number of trials is significantly lower than the number of recorded neurons. In this regime, for both synthetic and real data, we show that our method is competitive with data-hungry deep networks, with significantly improved uncertainty calibration over previous attempts to scale Bayesian methods. Our experiments provide a roadmap to neuroscience researchers in choosing from a host of potential dynamical latent variable models given key dataset properties and constraints.

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arXiv2025

Reverse Diffusion Sequential Monte Carlo Samplers

We propose a novel sequential Monte Carlo (SMC) method for sampling from unnormalized target distributions based on a reverse denoising diffusion process. While recent diffusion-based samplers simulate the reverse diffusion using approximate score functions, they can suffer from accumulating errors due to time discretization and imperfect score estimation. In this work, we introduce a principled SMC framework that formalizes diffusion-based samplers as proposals while systematically correcting for their biases. The core idea is to construct informative intermediate target distributions that progressively steer the sampling trajectory toward the final target distribution. Although ideal intermediate targets are intractable, we develop exact approximations using quantities from the score estimation-based proposal, without requiring additional model training or inference overhead. The resulting sampler, termed Reverse Diffusion Sequential Monte Carlo, enables consistent sampling and unbiased estimation of the target's normalization constant under mild conditions. We demonstrate the effectiveness of our method on a range of synthetic targets and real-world Bayesian inference problems.

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arXiv2025

Bayesian Invariance Modeling of Multi-Environment Data

Invariant prediction [Peters et al., 2016] analyzes feature/outcome data from multiple environments to identify invariant features - those with a stable predictive relationship to the outcome. Such features support generalization to new environments and help reveal causal mechanisms. Previous methods have primarily tackled this problem through hypothesis testing or regularized optimization. Here we develop Bayesian Invariant Prediction (BIP), a probabilistic model for invariant prediction. BIP encodes the indices of invariant features as a latent variable and recover them by posterior inference. Under the assumptions of Peters et al. [2016], the BIP posterior targets the true invariant features. We prove that the posterior is consistent and that greater environment heterogeneity leads to faster posterior contraction. To handle many features, we design an efficient variational approximation called VI-BIP. In simulations and real data, we find that BIP and VI-BIP are more accurate and scalable than existing methods for invariant prediction.

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arXiv2025

Variational Deep Learning via Implicit Regularization

Modern deep learning models generalize remarkably well in-distribution, despite being overparametrized and trained with little to no explicit regularization. Instead, current theory credits implicit regularization imposed by the choice of architecture, hyperparameters, and optimization procedure. However, deep neural networks can be surprisingly non-robust, resulting in overconfident predictions and poor out-of-distribution generalization. Bayesian deep learning addresses this via model averaging, but typically requires significant computational resources as well as carefully elicited priors to avoid overriding the benefits of implicit regularization. Instead, in this work, we propose to regularize variational neural networks solely by relying on the implicit bias of (stochastic) gradient descent. We theoretically characterize this inductive bias in overparametrized linear models as generalized variational inference and demonstrate the importance of the choice of parametrization. Empirically, our approach demonstrates strong in- and out-of-distribution performance without additional hyperparameter tuning and with minimal computational overhead.

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arXiv2025

Differentially Private Hyperparameter Tuning using Local Bayesian Optimization

Hyperparameter tuning is a key component of machine learning procedures, but when validation data contain sensitive user information, search mechanisms can leak private information through the selected configuration. Existing differentially private hyperparameter tuning methods often rely on near-random search, while prior differentially private Bayesian optimization approaches are typically global and, therefore, scale poorly with the hyperparameter dimensionality. We study differentially private hyperparameter tuning using local Bayesian optimization, focusing on settings where the validation objective is available only through noisy black box evaluations and gradients are unavailable or impractical to compute. We introduce DP-GIBO, a differentially private local Bayesian optimization framework that privately approximates gradients using a Gaussian Process surrogate. Under suitable conditions, we prove that DP-GIBO converges to a locally optimal hyperparameter configuration up to a privacy-dependent error, with dimensional dependence that is polynomial rather than exponential.Empirically, we show that DP-GIBO provides scalable private hyperparameter tuning across multiple tasks, substantially outperforming non-private random search and global Bayesian optimization baselines in moderate-to-high-dimensional hyperparameter spaces.

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arXiv2024

Computation-Aware Gaussian Processes: Model Selection And Linear-Time Inference

Model selection in Gaussian processes scales prohibitively with the size of the training dataset, both in time and memory. While many approximations exist, all incur inevitable approximation error. Recent work accounts for this error in the form of computational uncertainty, which enables -- at the cost of quadratic complexity -- an explicit tradeoff between computation and precision. Here we extend this development to model selection, which requires significant enhancements to the existing approach, including linear-time scaling in the size of the dataset. We propose a novel training loss for hyperparameter optimization and demonstrate empirically that the resulting method can outperform SGPR, CGGP and SVGP, state-of-the-art methods for GP model selection, on medium to large-scale datasets. Our experiments show that model selection for computation-aware GPs trained on 1.8 million data points can be done within a few hours on a single GPU. As a result of this work, Gaussian processes can be trained on large-scale datasets without significantly compromising their ability to quantify uncertainty -- a fundamental prerequisite for optimal decision-making.

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arXiv2024

Theoretical Limitations of Ensembles in the Age of Overparameterization

Classic ensembles generalize better than any single component model. In contrast, recent empirical studies find that modern ensembles of (overparameterized) neural networks may not provide any inherent generalization advantage over single but larger neural networks. This paper clarifies how modern overparameterized ensembles differ from their classic underparameterized counterparts, using ensembles of random feature (RF) regressors as a basis for developing theory. In contrast to the underparameterized regime, where ensembling typically induces regularization and increases generalization, we prove with minimal assumptions that infinite ensembles of overparameterized RF regressors become pointwise equivalent to (single) infinite-width RF regressors, and finite width ensembles rapidly converge to single models with the same parameter budget. These results, which are exact for ridgeless models and approximate for small ridge penalties, imply that overparameterized ensembles and single large models exhibit nearly identical generalization. We further characterize the predictive variance amongst ensemble members, demonstrating that it quantifies the expected effects of increasing capacity rather than capturing any conventional notion of uncertainty. Our results challenge common assumptions about the advantages of ensembles in overparameterized settings, prompting a reconsideration of how well intuitions from underparameterized ensembles transfer to deep ensembles and the overparameterized regime.

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arXiv2024

LoRA Learns Less and Forgets Less

Low-Rank Adaptation (LoRA) is a widely-used parameter-efficient finetuning method for large language models. LoRA saves memory by training only low rank perturbations to selected weight matrices. In this work, we compare the performance of LoRA and full finetuning on two target domains, programming and mathematics. We consider both the instruction finetuning (approximately 100K prompt-response pairs) and continued pretraining (20B unstructured tokens) data regimes. Our results show that, in the standard low-rank settings, LoRA substantially underperforms full finetuning. Nevertheless, LoRA better maintains the base model's performance on tasks outside the target domain. We show that LoRA mitigates forgetting more than common regularization techniques such as weight decay and dropout; it also helps maintain more diverse generations. Finally, we show that full finetuning learns perturbations with a rank that is 10-100X greater than typical LoRA configurations, possibly explaining some of the reported gaps. We conclude by proposing best practices for finetuning with LoRA.

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arXiv2024

Estimating the Hallucination Rate of Generative AI

This paper presents a method for estimating the hallucination rate for in-context learning (ICL) with generative AI. In ICL, a conditional generative model (CGM) is prompted with a dataset and a prediction question and asked to generate a response. One interpretation of ICL assumes that the CGM computes the posterior predictive of an unknown Bayesian model, which implicitly defines a joint distribution over observable datasets and latent mechanisms. This joint distribution factorizes into two components: the model prior over mechanisms and the model likelihood of datasets given a mechanism. With this perspective, we define a hallucination as a generated response to the prediction question with low model likelihood given the mechanism. We develop a new method that takes an ICL problem and estimates the probability that a CGM will generate a hallucination. Our method only requires generating prediction questions and responses from the CGM and evaluating its response log probability. We empirically evaluate our method using large language models for synthetic regression and natural language ICL tasks.

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arXiv2024

Approximation-Aware Bayesian Optimization

High-dimensional Bayesian optimization (BO) tasks such as molecular design often require 10,000 function evaluations before obtaining meaningful results. While methods like sparse variational Gaussian processes (SVGPs) reduce computational requirements in these settings, the underlying approximations result in suboptimal data acquisitions that slow the progress of optimization. In this paper we modify SVGPs to better align with the goals of BO: targeting informed data acquisition rather than global posterior fidelity. Using the framework of utility-calibrated variational inference, we unify GP approximation and data acquisition into a joint optimization problem, thereby ensuring optimal decisions under a limited computational budget. Our approach can be used with any decision-theoretic acquisition function and is compatible with trust region methods like TuRBO. We derive efficient joint objectives for the expected improvement and knowledge gradient acquisition functions in both the standard and batch BO settings. Our approach outperforms standard SVGPs on high-dimensional benchmark tasks in control and molecular design.

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arXiv2024

Pathologies of Predictive Diversity in Deep Ensembles

Classic results establish that encouraging predictive diversity improves performance in ensembles of low-capacity models, e.g. through bagging or boosting. Here we demonstrate that these intuitions do not apply to high-capacity neural network ensembles (deep ensembles), and in fact the opposite is often true. In a large scale study of nearly 600 neural network classification ensembles, we examine a variety of interventions that trade off component model performance for predictive diversity. While such interventions can improve the performance of small neural network ensembles (in line with standard intuitions), they harm the performance of the large neural network ensembles most often used in practice. Surprisingly, we also find that discouraging predictive diversity is often benign in large-network ensembles, fully inverting standard intuitions. Even when diversity-promoting interventions do not sacrifice component model performance (e.g. using heterogeneous architectures and training paradigms), we observe an opportunity cost associated with pursuing increased predictive diversity. Examining over 1000 ensembles, we observe that the performance benefits of diverse architectures/training procedures are easily dwarfed by the benefits of simply using higher-capacity models, despite the fact that such higher capacity models often yield significantly less predictive diversity. Overall, our findings demonstrate that standard intuitions around predictive diversity, originally developed for low-capacity ensembles, do not directly apply to modern high-capacity deep ensembles. This work clarifies fundamental challenges to the goal of improving deep ensembles by making them more diverse, while suggesting an alternative path: simply forming ensembles from ever more powerful (and less diverse) component models.

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arXiv2023

Posterior and Computational Uncertainty in Gaussian Processes

Gaussian processes scale prohibitively with the size of the dataset. In response, many approximation methods have been developed, which inevitably introduce approximation error. This additional source of uncertainty, due to limited computation, is entirely ignored when using the approximate posterior. Therefore in practice, GP models are often as much about the approximation method as they are about the data. Here, we develop a new class of methods that provides consistent estimation of the combined uncertainty arising from both the finite number of data observed and the finite amount of computation expended. The most common GP approximations map to an instance in this class, such as methods based on the Cholesky factorization, conjugate gradients, and inducing points. For any method in this class, we prove (i) convergence of its posterior mean in the associated RKHS, (ii) decomposability of its combined posterior covariance into mathematical and computational covariances, and (iii) that the combined variance is a tight worst-case bound for the squared error between the method's posterior mean and the latent function. Finally, we empirically demonstrate the consequences of ignoring computational uncertainty and show how implicitly modeling it improves generalization performance on benchmark datasets.

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arXiv2023

Practical and Asymptotically Exact Conditional Sampling in Diffusion Models

Diffusion models have been successful on a range of conditional generation tasks including molecular design and text-to-image generation. However, these achievements have primarily depended on task-specific conditional training or error-prone heuristic approximations. Ideally, a conditional generation method should provide exact samples for a broad range of conditional distributions without requiring task-specific training. To this end, we introduce the Twisted Diffusion Sampler, or TDS. TDS is a sequential Monte Carlo (SMC) algorithm that targets the conditional distributions of diffusion models through simulating a set of weighted particles. The main idea is to use twisting, an SMC technique that enjoys good computational efficiency, to incorporate heuristic approximations without compromising asymptotic exactness. We first find in simulation and in conditional image generation tasks that TDS provides a computational statistical trade-off, yielding more accurate approximations with many particles but with empirical improvements over heuristics with as few as two particles. We then turn to motif-scaffolding, a core task in protein design, using a TDS extension to Riemannian diffusion models. On benchmark test cases, TDS allows flexible conditioning criteria and often outperforms the state of the art.

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arXiv2023

Denoising Deep Generative Models

Likelihood-based deep generative models have recently been shown to exhibit pathological behaviour under the manifold hypothesis as a consequence of using high-dimensional densities to model data with low-dimensional structure. In this paper we propose two methodologies aimed at addressing this problem. Both are based on adding Gaussian noise to the data to remove the dimensionality mismatch during training, and both provide a denoising mechanism whose goal is to sample from the model as though no noise had been added to the data. Our first approach is based on Tweedie's formula, and the second on models which take the variance of added noise as a conditional input. We show that surprisingly, while well motivated, these approaches only sporadically improve performance over not adding noise, and that other methods of addressing the dimensionality mismatch are more empirically adequate.

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arXiv2023

Posterior Collapse and Latent Variable Non-identifiability

Variational autoencoders model high-dimensional data by positing low-dimensional latent variables that are mapped through a flexible distribution parametrized by a neural network. Unfortunately, variational autoencoders often suffer from posterior collapse: the posterior of the latent variables is equal to its prior, rendering the variational autoencoder useless as a means to produce meaningful representations. Existing approaches to posterior collapse often attribute it to the use of neural networks or optimization issues due to variational approximation. In this paper, we consider posterior collapse as a problem of latent variable non-identifiability. We prove that the posterior collapses if and only if the latent variables are non-identifiable in the generative model. This fact implies that posterior collapse is not a phenomenon specific to the use of flexible distributions or approximate inference. Rather, it can occur in classical probabilistic models even with exact inference, which we also demonstrate. Based on these results, we propose a class of latent-identifiable variational autoencoders, deep generative models which enforce identifiability without sacrificing flexibility. This model class resolves the problem of latent variable non-identifiability by leveraging bijective Brenier maps and parameterizing them with input convex neural networks, without special variational inference objectives or optimization tricks. Across synthetic and real datasets, latent-identifiable variational autoencoders outperform existing methods in mitigating posterior collapse and providing meaningful representations of the data.

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arXiv2022

Deep Ensembles Work, But Are They Necessary?

Ensembling neural networks is an effective way to increase accuracy, and can often match the performance of individual larger models. This observation poses a natural question: given the choice between a deep ensemble and a single neural network with similar accuracy, is one preferable over the other? Recent work suggests that deep ensembles may offer distinct benefits beyond predictive power: namely, uncertainty quantification and robustness to dataset shift. In this work, we demonstrate limitations to these purported benefits, and show that a single (but larger) neural network can replicate these qualities. First, we show that ensemble diversity, by any metric, does not meaningfully contribute to an ensemble's uncertainty quantification on out-of-distribution (OOD) data, but is instead highly correlated with the relative improvement of a single larger model. Second, we show that the OOD performance afforded by ensembles is strongly determined by their in-distribution (InD) performance, and -- in this sense -- is not indicative of any "effective robustness". While deep ensembles are a practical way to achieve improvements to predictive power, uncertainty quantification, and robustness, our results show that these improvements can be replicated by a (larger) single model.

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arXiv2022

Invertible Gaussian Reparameterization: Revisiting the Gumbel-Softmax

The Gumbel-Softmax is a continuous distribution over the simplex that is often used as a relaxation of discrete distributions. Because it can be readily interpreted and easily reparameterized, it enjoys widespread use. We propose a modular and more flexible family of reparameterizable distributions where Gaussian noise is transformed into a one-hot approximation through an invertible function. This invertible function is composed of a modified softmax and can incorporate diverse transformations that serve different specific purposes. For example, the stick-breaking procedure allows us to extend the reparameterization trick to distributions with countably infinite support, thus enabling the use of our distribution along nonparametric models, or normalizing flows let us increase the flexibility of the distribution. Our construction enjoys theoretical advantages over the Gumbel-Softmax, such as closed form KL, and significantly outperforms it in a variety of experiments. Our code is available at https://github.com/cunningham-lab/igr.

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arXiv2022

Scaling Structured Inference with Randomization

Deep discrete structured models have seen considerable progress recently, but traditional inference using dynamic programming (DP) typically works with a small number of states (less than hundreds), which severely limits model capacity. At the same time, across machine learning, there is a recent trend of using randomized truncation techniques to accelerate computations involving large sums. Here, we propose a family of randomized dynamic programming (RDP) algorithms for scaling structured models to tens of thousands of latent states. Our method is widely applicable to classical DP-based inference (partition, marginal, reparameterization, entropy) and different graph structures (chains, trees, and more general hypergraphs). It is also compatible with automatic differentiation: it can be integrated with neural networks seamlessly and learned with gradient-based optimizers. Our core technique approximates the sum-product by restricting and reweighting DP on a small subset of nodes, which reduces computation by orders of magnitude. We further achieve low bias and variance via Rao-Blackwellization and importance sampling. Experiments over different graphs demonstrate the accuracy and efficiency of our approach. Furthermore, when using RDP for training a structured variational autoencoder with a scaled inference network, we achieve better test likelihood than baselines and successfully prevent posterior collapse. code at: https://github.com/FranxYao/RDP

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